Atomic resolution insight on Sac7d protein binding to DNA and associated global changes by Molecular Dynamics Simulations

Sac7d is a small thermostable protein that induces large helical deformations in DNA upon association. Starting from multiple initial placements of the unbound Sac7d structure relative to a B‐DNA oligonucleotide molecular dynamics (MD) simulations were employed to directly follow several successful binding events at atomic resolution that resulted in structures in close agreement with the native complex geometry. The final native complex formation occurred rapidly within tenth of nanoseconds and included simultaneous large scale kinking, groove opening, twisting and intercalation in the target DNA. The simulations indicate that the complex formation process involved initial non‐native contacts that helped to reach the final bound state with residues intercalated as the center of the kinked DNA. It was also possible to identify several long‐lived trapped intermediate states of the binding process and to follow sliding processes of Sac7d along the DNA minor groove.

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